My $0.02
I would say that most fishermen find GPS useful when combined with the Si sonar. Now with DI or 2D sonar you can always use your handheld GPS to mark the location since you will be directly over the structure you see on your sonar (or very close to it). The Si sonar allows you to see structure from hundreds of feet away. With the GPS combined with the Si sonar you can mark structure you see out to either side 100+ feet away without having to travel over it. This is helpful when you see something but do not have time to run over it and also when someone else is fishing it…

I prefer the external GPS because you can mount the GPS Receiver closer to the transducer which allows you to take some of the position inaccuracy out of your marked waypoint. When you mark a waypoint using sonar (any type of sonar) the unit assumes that the GPS Receiver and the transducer are in the same location. Having them separated by six feet or more could introduce an inaccuracy of up to double that distance. I would want my sonar-GPS system to have the best possible accuracy when marking and traveling back to waypoints, so the external GPS would be the best option here – unless this is for a bow mounted unit in which an internal GPS would be fine (since it would be located close to the trolling motor mounted transducer).